The main interface of JBrowseR
involves using the View
component. An introduction to using
this interface can be found here.
JBrowseR has several R functions for generating configuration to pass to
the View
component. Under the hood, these functions are
returning strings of JBrowse 2 JSON configuration.
While JBrowseR supports the majority of JBrowse 2 configuration and
greatly simplifies usage, it does not support the entire configuration
API. If you find yourself wanting to do something unique or custom that
JBrowse 2 supports but isn’t provided by the View
component, you can use the JsonView
component. This
component can be passed a full JSON configuration as an argument.
This is what the JSON configuration for an assembly looks like:
{
"assembly": {
"name": "Sars-Cov2",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "Sars-Cov2-ReferenceSequenceTrack",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"uri": "https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz"
},
"faiLocation": {
"uri": "https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz.fai"
},
"gziLocation": {
"uri": "https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz.gzi"
}
}
}
}
}
Let’s see how this compares to the configuration generated JBrowseR:
library(JBrowseR)
assembly(
"https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz",
bgzip = TRUE
)
## [1] "{ \"name\": \"sars-cov2\", \"sequence\": { \"type\": \"ReferenceSequenceTrack\", \"trackId\": \"sars-cov2-ReferenceSequenceTrack\", \"adapter\": { \"type\": \"BgzipFastaAdapter\", \"fastaLocation\": { \"uri\": \"https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz\" }, \"faiLocation\": { \"uri\": \"https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz.fai\" }, \"gziLocation\": { \"uri\": \"https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz.gzi\" } } } }"
JBrowseR generates equivalent JSON for the same assembly. This gives a better understanding of what is happening when generating JBrowse 2 configuration using JBrowseR.
JsonView
Now, if we have a JSON file config.json
containing the
configuration above, we can parse it and use it to configure a browser.
Here is what this looks like:
library(shiny)
library(JBrowseR)
ui <- fluidPage(
titlePanel("JSON JBrowseR Example"),
JBrowseROutput("browserOutput")
)
server <- function(input, output, session) {
# using JBrowseR helper function to parse the config
config <- json_config("./config.json")
output$browserOutput <- renderJBrowseR(
JBrowseR("JsonView",
config = config,
location = "NC_045512.2:1..2,000"
)
)
}
shinyApp(ui, server)
Here are some great resources for learning more about JBrowse 2 configuration:
One important point when looking at JB2 config files is that the main app accepts an array of assembly objects. On the other hand, the React LGV component only accepts one assembly object, since it is a single linear genome view. Since JBrowseR is powered by the LGV component, it also only accepts a single assembly.